All in Good Time
by L-shadows8
Summary: It has been 12 years since the GIW took Danny. Now, a war on ghosts is looming and time is running out. With all efforts exhausted, what does Clockwork have up his sleeve? And what does a 15 year old girl in California have to do with it? Post PP, secret not revealed. Rated M because I'm paranoid.
1. Chapter 1

**Hey everyone! This is my first fic! Yay! Reviews and comments are welcome. Thanks for reading!**

 **I do not own Danny Phantom! Danny Phantom belongs to Butch Hartman. OC characters are mine.**

Bethany tapped her pencil on her desk as she sat with her head in her hand. The class seemed to drag on and on, the clock standing still. Finally, after what seemed like ages, the bell rang. The students hurried out of the classroom, eager to get home on the gorgeous Friday afternoon outside. Bethany made her way to her locker, where her friend Seth was waiting for her.

"Hey you" he called with one of his sweet smiles that could melt anyone's heart.

"Hey yourself" Bethany quipped back with a smirk.

"What are you feeling on this fine Friday? Movie, beach, mall?"

As they talked, they walked through the front doors of the school and out into the sunlight. Bethany squinted and shielded her eyes with her hand. "Definitely the beach."

Seth smiled and clapped his hands like a little kid. "Awesome! I was hoping you would say that! I want to try out a new surf board I got."

Bethany smiled knowingly at her best friend of 10 years. Growing up together, she was sure Seth knew her better than she knew herself, the same way she knew him. Seth has loved to surf ever since he could hold a surfboard. Growing up in California, it was one of the common past times of the high school students in the area. While he wasn't the most athletic person, he could pull some decent stunts.

"Sounds good. I'll bring my book."

"Did you get much sleep last night? You seem exhausted."

Bethany sighed. He really did know her so well.

"I've been having the nightmare again," she mumbled. Seth instantly looked concerned.

"Same thing? Or has it gotten worse?" She shrugged. She hated talking about the nightmare she has had ever since she was a kid. It made her feel weak. She hated feeling weak.

"Just the same. It's fine really. How about we go grab our stuff and meet back up at the beach?"

Seth looked ready to protest Bethany's giving up so easily but he decided to let it slide. He knew if it were serious, she would speak up. Shrugging, Seth replied, "Sounds like a plan. See ya!" He waved as they went their separate ways.

Bethany walked home, thinking deeply about her previous night and what it could possibly mean. It had never happened so frequently before. She walked in her front door; forehead creased with worry, and made her way into the kitchen for some food. Her mom was already working on dinner and she looked up from the island, where she was cutting vegetables, to greet her daughter with a smile.

"Hey Beth, how was school?"

"Oh, um, it was fine. Nothing special." Her mother instantly noticed the distracted tone. She set down her knife and began to eye her daughter closely.

"Is everything alright?" She tested the waters. Bethany waved her hand aimlessly in the air.

"Yeah, yeah everything's fine. I'm going to head to the beach with Seth." Bethany distractedly grabbed an apple off the counter and turned to leave the kitchen. Her mother knew something was up and she hopped Bethany would be more willing to talk after some down time at the beach with Seth.

"Alright. Have fun! Don't be late for dinner!" Her mom watched her leave and resumed cutting the vegetables, trying to think of what could be on her daughter's mind.

Bethany felt guilty for blowing off her mom like that, but she really didn't know how to even begin to talk about it. Her parents knew about the nightmare, she was always very open with them, but the worried looks they got whenever she mentioned it broke her heart. Bethany didn't want them to fuss over her. She loved her parents and they had always been supportive. Bethany hated making their lives harder. Despite her guilt, she turned up the street towards the beach, hoping her book and some sun would relieve her troubled mind.

Seth walked up to where Bethany lay on her towel, reading. He shook off his wet, sandy blonde hair on her much to her annoyance and his enjoyment.

"Ugh, Seth really?"

"Come on, you know I live to make your life hell" he teased.

Bethany huffed. "Whatever" she mumbled.

"So did you hear about the ghost sighting a few days ago?"

Bethany paused in the line she was reading but didn't look up from the book. "No, why?"

"They said it attacked someone's home; had to call the real deal ghost hunters to get it. The officials say they were lucky no one was hurt. Scary shit, huh?"

Bethany shrugged, still looking at her book. "If you say so."

"Aw come on!" Seth tossed her one of his famous puppy dog eye faces. "You can't tell me you don't think that's pretty freaky and interesting!"

"No not really," she replied in a bored tone. "Ghosts are just something the school tells us to be fearful of in order to keep us from doing something stupid. To keep us 'in line'."

"Aw, you know that's never stopped me before," Seth responded in a light tone as he nudged Bethany's shoulder. She sideways glanced at him with a small smile and playfully nudged him back. She turned back to her book as Seth squinted and looked out onto the ocean.

"What do you think of it all?" He inquired in an uncharacteristically serious tone.

"What do I think of what?"

"You know, the whole ghost thing; what they teach us in school. That all ghosts are evil and all that jazz." Bethany sighed and put down her book, also joining Seth in staring out into the vast waters.

"I don't know. I don't really have an opinion."

"But what about all that mess in Amity Park? They have no justification for locking him up!"

"How do you know?" She counted sharply. "How do you know he wasn't working with Plasmius?"

"Seriously Beth? You're just like the rest of them." His last words came out in a mutter.

"Excuse me? Sorry I don't give a rat's ass like you Seth. Besides, that happened a long time ago. He's probably dead or whatever happens to ghosts when they disappear by now." She picked her book back up and tried to resume reading.

"Yea, he probably is." Silence resumed between the two as they soaked up the last of the evening sun.

* * *

Bethany returned home just in time for dinner. Her parents were laughing in the kitchen as she walked in the front door. Her dad stuck his head in the doorway and greeted her warmly.

"Hey kiddo! It's about time, I'm starving!" He ducked back in the kitchen and Bethany laughed to herself. Her dad was the type of person who spoke without a filter, never realizing the consequences of what he said. She dropped her backpack on the floor by the table and slide into her spot, eyeing the meal in front of her. Once her parents joined her at the table, they all dug in.

"So kiddo," her dad asked around a bite of food, "how was school?"

"Oh you know, same old same old. Kind of like you." She smirked as her father feigned offense. Her mom gave her a look but was smiling at the same time, used to her husband and daughter's sarcastic quips.

"Aw, you know you love your old man. Well today at work was interesting! We had a new guy start today. Says he's from Amity Park, the ghost town." Her mother nodded with interest and Bethany stared intently down into her plate, not wanting to continue her conversation from earlier with Seth.

"Yeah, it's crazy! He says they want to end all ghosts or something. You know, to make the world safer and all that. I just can't imagine living there with all of the attacks. Seems like if you have any common sense then you should just move away." He shoved another forkful of food in his mouth as he spoke and Bethany continued her staring contest with her meal. Something in her suddenly snapped and she was overcome with exhaustion. Dropping her fork and scooting out from the table abruptly, Bethany muttered an, "I'm not hungry," and fled up the stairs before either of her parents could speak. She shut her door tightly and collapsed on her bed, suddenly too tired to do anything.

Back in the kitchen, her parents looked at each other with baffled expressions. Little did Bethany know that the universe was shifting, and as her parents resumed eating, they were already beginning to forget her.

That night, Bethany lay in her bed, caught in a nightmare.

 _It was dark save for a dull light coming from the moon through the window. She heard worried whispering in the room. Suddenly there was a crash and the sound of running footsteps. A scream was heard and more fighting sounds. Bethany looked to her right and suddenly saw a pair of red eyes. She didn't have time to scream._

She shot up in bed, her head pounding and her clothes sticky with cold sweat. This was the fourth night in a row she thought with concern. It had never occurred so frequently before. She sighed and lay back down on her side, knowing that sleep wasn't coming any time soon.

The next thing Bethany knew, her phone was blaring with the sound of Seth's ringtone. She quickly answered to let him know she was up and began to get ready for the day.

* * *

Sam paced her living room floor as the newscast continued to cover the ghost attack happening downtown. Her hands clenching and unclenching as she paced, her mind muddled. Suddenly, there was a knock at the door, startling her out of her pacing. Sam walked over and looked through the peephole, seeing Tucker standing outside, a worried look on his face. She immediately opened the door.

"It's bad isn't it?" She asked as he walked in. Ever since Danny had been taken, Tucker tried to be gentle with Sam. As he bit his lip, thinking of how to say it, Sam grew irritated.

"Tucker, I am all grown up. Just spit it out. I can handle it." She stared him down, watching him process his thoughts. Finally, he let out a sigh and rubbed his eyes.

"It's getting worse. Valerie told me that they have almost perfected their weapons systems. It doesn't help that the ghosts won't ever take a break…" His eyes shifted to the side, avoiding Sam's gaze.

"And Danny?" Sam's heart spiked at the mention of her husband and his state. Tucker sighed again and shuffled his feet, clearly uncomfortable.

"He…they….its…basically, he's prepared to help them. You know,"

"Damnit! Doesn't he know we can fight for ourselves! He can't possibly be on their side!" Sam resumed pacing, muttering under her breath.

"Sam, its Danny we're talking about. If there were any threat whatsoever to his family, or us you know he would risk everything. Including his loyalty to the Ghost Zone." Tucker quieted as his last statement sunk in. Sam stopped pacing and glared at the floor, fighting tears.

"There has to be something we can do." She whispered, more to herself than Tucker. He walked over to her and enveloped her into a hug. She buried her head into his chest and shut her eyes.

"I know Sam. We will get him out. I won't rest until we do. We just need a plan that will work. Valerie has been helping immensely but there is only so much she can do." Sam nodded her head, not leaving Tucker's embrace.

Ever since Danny was taken by the Guys in White, Sam, Tucker, his family, and Valerie had tried numerous times to get Danny out. Each time ended in failure. The GIW had him under maximum security and although Valerie worked for the GIW, there was only so much she could do undetected. Valerie threatened to quit when she learned of Danny's capture, as she had learned of his secret during their college years, but Tucker convinced her to stay in order to help them gather information from the inside.

All they knew so far was that Danny was kept in maximum security, his energy being harvested for weapons. He was the main weapon, though. The GIW told him they would not hesitate to kill everyone he loved if he refused to help. It was the final pawn in the GIW's attempt to eradicate the world of ghosts once and for all. Sadly, most of the public was on board with this too.

Sam finally released Tucker and wiped her eyes. She let out a huff of breath and sat down on her living room couch. Tucker joined her and they resumed watching the newscast, as the GIW finally caught the nuisance ghost.


	2. Chapter 2

**Here is chapter two! I have a few more written and will upload them soon!**

 **I do not own Danny Phantom! Danny Phantom belongs to Butch Hartman. OC characters are mine.**

Seth was waiting on the sidewalk outside of Bethany's home, casually scrolling through his phone. When he saw her walking out her front door, he pocketed his phone and smiled.

"Well, it's about time slow-poke!" He gave her a cheeky grin and she lightly punched him in the shoulder once she was next to him.

"Ha-Ha, you are hilarious." Bethany deadpanned. She was exhausted from her restless night and was struggling to find the energy to keep up with Seth's antics. He broadly smiled back to Bethany.

"Don't I know it!" The two lapsed into a comfortable silence as they walked. It was Saturday and they were heading to a local plant nursery for required community service hours by their school. She would have been grumpier if Seth wasn't going with her. Ten minutes later, they arrived at the nursery and were assigned a row of plants to pick weeds. The two stood side-by-side, occasionally nudging each other and exchanging playful smiles. After a time, Seth couldn't fight his curiosity anymore.

"So," he cleared his throat and dared a sidelong glance at his best friend. "I have a theory." Bethany continued pulling out weeds, making no move to face Seth.

"Mmhmm?"

"It's about Phantom…" Bethany abruptly pulled out a chunk of weeds and, consequently, a chunk of soil along with it. She frowned to herself. Seth continued on, gaining momentum.

"You see, I find it really odd that the people there are so okay with him disappearing. I mean it was obvious he was helping them, right? So there has to be someone else trying to get rid of him." He waved his hands around as he spoke, getting excited about this theory. Bethany continued pulled weeds, refusing to look over at Seth.

"So that had me thinking, who could-," suddenly a chill ran down Bethany's spine and her head snapped up just in time to see a box flying towards her. She grabbed Seth by the arm and yanked him down, watching as the box flew over their heads right where they had been standing. Slowly peeking over the row of plants, Bethany saw a blue figure floating a few rows in front of them, wearing overalls and a gray hat. He smiled maliciously at them and proceeded to raise his hands and shout, "Beware!" Just as he did so, another box came flying at them, causing Bethany to duck down again.

"Seth, I think it's a ghost! We need to move, now!" She began crawling towards the main building next to the outdoor rows of plants and Seth followed suit. His face was torn between excitement and fear. Boxes continued to fly overhead as they moved. Suddenly, the ghost was floating above them, cackling like a maniac.

"You two cannot escape my cardboard boxes of doom!" He summoned two more boxes and Bethany and Seth stood to make a break for it. They just made it behind the building's wall as the two boxes smashed into it. The pair bolted for the end of the room and flipped over a long table to hide behind. Panting, they sat with their backs to the outside, hoping the ghost wouldn't find them.

"What the hell…" Bethany whispered, still catching her breath. Seth only nodded in response. Seth peered over the table and saw the ghost looking around, a few boxes floating behind it.

"This is the second one this week. This never happens this far from Amity." He muttered.

"I told you they were evil." Bethany huffed, her anger growing. Seth was opened his mouth to respond when suddenly, a box flew over their hiding spot and crashed into the wall across from them. They both jumped and looked up to see the ghost floating above.

"You puny humans cannot defeat me! For I am the Box Ghost!" He raised his arms above his head again and something in Bethany snapped.

"What are you even doing here?" She spat angrily, surprising herself and Seth with the sudden outburst. The ghost seemed confused, as if the answer were obvious.

"It is no longer enjoyable in Amity Park, puny human. Now that he is locked up, we came here, for the next best thing!" Now it was Bethany's turn to look confused. What was he talking about, _the next best thing_? Just as the ghost summoned two more boxes, he was shot by a blast and slammed into the wall. The three of them were startled and looked back to the entrance of the building to find the source of the shot. Three men in white uniforms stood there, one holding a smoking weapon. It looked like a high-tech gun. The ghost clearly recognized them because a look of fear crossed his face and he fled through the roof. The men took off after him, leaving a stunned Bethany and Seth to sit in silence.

* * *

Their walk home later that day was full of tense silence, both teens lost in their own thoughts. By the time they reached Bethany's home, Seth hardly registered her leaving. He looked up with a confused expression and it took him a moment to remember where he was.

"Oh, right, uh bye Beth. I'll see you," He awkwardly waved and continued on his way, leaving a very confused Bethany to watch him go. Seth was not one to be quiet after big events like a ghost attack. He seemed off somehow. Shrugging off her curiosity, she made her way inside her house and into the kitchen. Her parents were at the table eating homemade sandwiches for lunch. They were sweaty from doing yard work, the standard Saturday activity, and they had dirt and grass stains on their clothes. She greeted them and went to find the sandwich they undoubtedly made for her. All she found on the island was various ingredients lying out, but no sandwich. Confused, she turned back to her parents.

"Uh, hey, did you forget about me? Where's my food? Or did dad already eat it all?" She smirked at her father but the smile slowly faded when she noticed her parents' confused expressions. They were looking at her like they had no idea who she was. Bethany shifted her feet, suddenly very uncomfortable. Her father closed his eyes and slapped his forehead.

"Oh, gosh, duh! How did I forget?" He stood up to make her lunch with a dazed expression, clearly shocked that he managed to forget a basic weekend ritual. Her mom seemed to come too as well, shaking her head at herself.

"Gosh, sorry Beth! The sun must be getting to us…" She mussed to herself. This was all starting to feel very eerie. First, Seth barely registered Bethany's house and now her parents? Something was very wrong. She decided to try something else.

"So there was a ghost at the plant nursery today. Seth and I saw it." Her mom looked up, still seeming confused.

"What is a ghost doing all the way out here?" Bethany shrugged, still unnerved by the lack of concern. Her parents should be asking question after question, ensuring she was all right. Instead, they treated it like any other small talk. Her father handed her the finished sandwich and sat back down at the table. His usual banter missing. Something was wrong, and Bethany began to feel very uneasy about this whole situation.

"I'm going to eat in my room," She stated and began backing out of the kitchen. Her parents continued eating and hardly noticed, only muttering an "okay" as she left. Making her way upstairs to her room, Bethany began to wonder if maybe she was going insane, or if that interaction had really just happened.

* * *

Valerie swiped her key card and the door unlocked and slid open. She stepping inside and stood in front of the agent's desk, awaiting her instructions. Agent K casual looked up from the file he was reviewing, smiling as he saw his employee.

"Ah, yes, hello Valerie. I'm assuming you're here because you talked to Agent M?"

"Yes, sir. What is it you need me to do?" Valerie clenched and unclenched her fists, losing patience with her superior. Ever since Danny had been captured, interacting with her boss was about as enjoyable as having teeth pulled. Agent K set down the folder containing the file and took off his dark glasses to set them on his desk, his dark eyes scanning Valerie, calculating.

"Yes, well, it seems our plan is almost complete. However, there has been a slight complication. I need you to do some digging." He gazed at Valerie, measuring her reactions.

"Digging for what, exactly?" She held steady, preparing for anything the Agent might say.

"It seems that Daniel has mentioned something a few times now. He keeps asking 'where she is' and 'what did you do with her'. When probing further, he just keeps asking those same things, claiming we should know what he is talking about. We are worried about his pressing concern. This person could be a threat to our operation."

"And you want me to figure out who he is talking about?" Valerie stood with confusion written on her face. She knew that Sam was safe in Amity and Dani was instructed to stay clear of the area, for fear of her capture as well. Jazz and Danny's parents were also fine, Valerie had spoken with them just yesterday. Agent K smiled, an expression of approval crossing his face.

"I knew I liked having you work for me." Valerie internally cringed at his praise, wishing she could punch him right then and there. However, a more pressing thought stopped her from acting on that desire.

"Wait, if you expect me to find out who he means, then does that mean you want me to talk to him directly?"

"Yes, however we will be outside of the room listening in on the conversation. For security reasons of course." He nonchalantly folded his hands and awaited her response. Valerie shifted her stance, weighing her options.

"With all due respect sir, that is exactly what Danny would expect. If you hope to get more information from him, you need to let me go in alone." Agent K's expression was emotionless, clearly deciding how much he trusted his top employee. Finally, he let out a breath and eyed Valerie warily.

"I understand and of course you are right. I have been hesitant to initiate contact between you two because of your familiar history." Valerie fidgeted slightly, uncomfortable with his analysis.

"Yes, however I am loyal to the GIW. I made that clear when I stayed with you after finding out about Danny's secret and his capture." Agent K nodded to himself, pleased with her response.

"Very well. I will set up the exchange." Valerie nodded and left the office, already determining the fastest route to Sam's home.


	3. Chapter 3

**Chapter three! I promise the back story stuff is almost over and things will get rolling soon! Thanks for reading!**

 **I do not own Danny Phantom! Danny Phantom belongs to Butch Hartman. OC characters are mine.**

 _It started as it always did in the room. But this time it was more clear. She felt as if she was actually there._

 _"What should we do?" She heard a female voice ask._

 _"I don't know. We know people are becoming uneasy. They want me gone..." A male voice answered. Suddenly a crash sounded. Panicky the female voice said, "They're here. What are they doing? We have to do something!" The voices left the room towards the sounds out of the room. Again, Bethany turned to the right and saw the eyes, the eyes that plagued her nightmares._

 _"It is time you come with me."_

Bethany woke with a scream in her throat. She took deep breaths to calm her racing heart. Suddenly, a cold chill swept the room and she knew something wasn't right. She slowly turned her head to the right and saw red. The ghost has an eerie glow and floated calmly, its lack of legs doing nothing to keep Bethany's panic away. It seemed to be carrying a staff of some sort and it wore a strange purple cloak. She noticed something that look like clocks _inside_ its chest. The scream wouldn't escape her and she sat paralyzed by fear.

"It is time you come with me." Next thing she knew, she passed out and everything went black.

As Bethany slowly came too, she first noticed the faint sound of ticking in the background. She was on a coach in some sort of study. Looking out the window she saw a swirling green sky. _I'm in the ghost zone._ Her original panic began to resurface as she quickly got up and fled the room. She entered a larger room, filled with various viewing screens. The same ghost from earlier floated nearby, watching a screen.

"Hello Bethany" it said without turning around. She held her ground and said nothing. The ghost sighed.

"I'm sure you would like to know why you are here. I will start by introducing myself. My name is Clockwork and I am the ghost of Time." He paused but she continued the silent treatment. He turned to face her and continued speaking.

"The time has come for you to return to your past." Bethany's brow furrowed.

"What are you talking about?"

"There is no way for me to explain this without shocking you. Therefore I will do my best to tell you clearly." Her heartbeat picked up at his words.

"I know you have learned of ghosts in your schooling, especially two: Vlad Plasmius and Danny Phantom."

"Yea we had to take a class about all of the ghosts. What does this have to do with me?"

"As you know, Danny Phantom was captured by a group of rouge agents almost 12 years ago. He is still alive, being held so he can be used as a weapon in the war against ghosts." Bethany raised her eyebrows.

"A war against ghosts? Why? And how can they use him?"

Clockwork turned back to the viewing screen. "They threaten to harm his family if he does not cooperate. He is the best chance they have of winning this war. As you already know, humans do not think kindly of ghosts." Bethany suddenly felt a wave of guilt. Maybe Seth was right about her. She was just like everyone else. Clockwork turned back to her with a serious expression.

"This is where you come in. You need to free Daniel so he can help stop this group and prevent a war."

"Umm in case you haven't noticed, I'm a 15 year old girl. How can I possibly free him?"

Clockwork smirked. "You would be surprised. After all, I would think you would want to save your father."

"My…my what?" Bethany's jaw dropped, her eyes grew to the size of dinner plates. "My dad…is Phantom…he's…but he's evil! And a ghost! He can't be my dad!"

"Please let me continue explaining. Danny Phantom is a unique ghost. He is actually only half ghost. The other half is human. An accident in his teen years left him in that state. Half dead and half alive."

Bethany eyed Clockwork as if he had grown two heads, although for a ghost that probably wasn't abnormal. She tried to form words or questions or anything to react but her mouth simply kept moving, opening and closing over unknown words. Clockwork continued on, knowing she had knowing to say.

"Now, of course the public does not know this fact, otherwise his capture would have drawn more controversy. However the Guys in White, the organization that took him, were able to figure this out. The night in your dreams is the night he was taken."

"So how did I end up in California?"

"That was where I came in." Suddenly she recognized where she had seen those eyes before. _It is time you come with me._ "It was you…you took me." Bethany felt her head spin and before she knew it, she vomited on the floor. Clockwork waited patiently for her to regain her composure, going back to watch some of the viewing screens as she did so.

Bethany wiped her mouth with a shaking hand and stood up. Cautiously, she walked over to this Clockwork ghost and stood next to him. Quietly, she spoke up.

"I don't have any…ghost….abilities…I guess. How do you know I can actually help with anything?"

Clockwork had a small smile on his face. "I will train you of course."

Bethany remained skeptical, shaking her head slightly. "If you say so."

To that, Clockwork smiled again. "Shall we begin then?" He led her over to a viewing screen showing a large dark gray building. The words "Guys in White" was written on the side in large, black letters. Bethany already had a bad feeling about them. Clockwork waved his staff, drawing the view inside the building through various hallways and floors until a room was reached.

"This is your father's room. He is being held here, under constant watch with various security measures."

"So he's being held in the GIW headquarters in Amity, with maximum security and numerous guards and weapons? And you want me to free him?" Bethany sat with a perplexed expression, mouth slightly open with wide eyes. It amused Clockwork. Her confused facial features reminded him of Daniel whenever Clockwork cryptically spoke with him.

"The headquarters are impenetrable for ghosts. And with the security measures, only top officials can gain access into his room. This is where you come in. You have the abilities to go through the walls and into his chambers, but in human form, you won't set off any ectoplasmic alarms." She stared at him cautiously.

"Okay, got it…"

* * *

Learning about her father's secret had not been easy. Well, learning any of this had not been easy. Clockwork showed Bethany the accident on one of his viewing screens, Danny Fenton going into the portal and Danny Phantom coming out. He showed her Danny defeating numerous ghosts and even him and Sam falling in love. He also unlocked the mystery of her nightmare, showing her the scene of Danny's capture when she was only 3 years old. Sam and Danny had been worryingly talking in her room as she slept. Suddenly, the GIW broke down the door, _the crash in her dream,_ and stormed the house. While Danny and Sam put up a good fight, it wasn't enough. The GIW had come prepared.

It took her some time to process everything she saw on those screens. Bethany always knew she was adopted. Her parents made an effort to tell her the truth early on to prevent any harm later. It became increasingly obvious as she grew up too, her dark, jet-black hair and blue eyes nothing like her parents' blonde hair and brown eyes. She loved her parents dearly. Never in her wildest dreams did Bethany guess that her birth father was Danny Fenton/Phantom.

Clockwork was patient with her. He went over the plan as slowly as she needed, allowed her time to process, and handled the difficult topics with grace. Bethany surprised herself with how quickly she grew to trust Clockwork.

"So, shall we start training your powers?" Bethany raised an eyebrow and shrugged her shoulders.

"I guess so." Clockwork chuckled and led her to a bigger room with space to practice. And so they began. Clockwork decided to start with the easiest powers: invisibility and intangibility.

"Focus on the cold feeling inside your chest and let it expand throughout your body. Imagine you are the only solid thing in this world and everything else is impalpable. You can pass through any surface at will." Bethany found herself holding her breath as she tried to imagine this. Her forehead creased with concentration and her hands moved into fists. Despite the effort, she didn't become intangible. Bethany let out a huff of frustration and looked over to Clockwork, giving him an exasperated expression. Clockwork only chuckled.

"You must be patient. These are not abilities that will be easy to bring forth." It amazed Clockwork how much he saw both of Bethany's parents in her. The stubbornness of not being able to gain a skill quickly was something Danny always displayed. Her ability to adapt to this new situation was a trait Sam exhibited, something that had saved the trio numerous times when things took an unexpected turn. It made Clockwork guilty, knowing he had to take her away from her parents and wait this long. It was the only way, though. This timeline was the only one that could prevent a war. An aggravated groan drew Clockwork from his musings and he looked back over to see Bethany trying again.

She tried to close her eyes and mentally picture the world blurring out, with her as the only solid being. She tried conjuring up the cold feeling and letting it spread throughout her body. She tried everything she could think of and got nowhere. It left her angry, defeated, and overall exhausted. Clockwork sensed that Bethany had reached the end of her rope and floated over to lay a hand on her shoulder.

"It is alright. I think some rest would do you well. We can try again tomorrow." She simply nodded, continuing to stare down the wall across from her and making no move to face Clockwork. He led her out of the room and into another small space, with a bed and a dresser set up in the corner and a bathroom across from the bed. She stepped inside and turned to mumble a "thanks" before Clockwork left her be. Of course he knew when she would finally gain access to her powers. Clockwork knew everything. This also meant that he knew what he needed to say to push her in the right direction.

"It will come to you. All in good time." He floated back to the main viewing room and resumed his duties.

* * *

That night, Bethany's sleep was interrupted by a new dream.

 _She stood in a dark room with her parents from California standing in front of her. Out of the darkness, two new people stepped next to her parents. Bethany did not recognize them._

 _"Choose." Her mother said in a monotone voice. It unnerved Bethany and she gave her mom a confused look._

 _"Choose what? What are you talking about?" Her parents and two strangers continued standing there, emotionless._

 _"Choose." This time it was her father who spoke, his empty voice nothing like his normal loud, booming voice that loved to tell cheesy dad jokes and talk about baseball. Bethany was growing more and more uneasy. She still didn't understand._

 _"It is us, or them." Her mother spoke again and Bethany finally began to understand. The two strangers were her real parents. It was obvious now. They had dark hair, like Bethany's jet black, and she had the same blue eyes as her father. Her pale skin matched the stranger's shade as well._

 _"No. I don't want to choose." She took a step back, suddenly very afraid. The two sets of parents simply stepped back out into the darkness, leaving Bethany alone and confused._

 _"Wait!" She cried. "Please don't leave me here! Wait!" She grew panicked and in the dark room all alone, she realized she didn't know who she belonged to._


	4. Chapter 4

**Chapter four! Thanks for reading!**

 **I do not own Danny Phantom! Danny Phantom belongs to Butch Hartman. OC characters are mine.**

The door to the chamber slid open and Agent K strode in.

"Well good morning. Are we ready for today's test?"

Danny, currently in human form, glared at the agent, with his spotless uniform and cool, condescending demeanor. It pissed him off, even now after seeing this man for 12 years. Agent K just scoffed.

"Well I see someone woke up on the wrong side of the bed today." He motioned for the guards to take Danny to the testing rooms. The guards each roughly took one of Danny's arms and led him into the adjacent testing room. By now, he knew the sections of his chamber by heart. It was what the GIW was testing each time they led him in here that was still a mystery. This time, Danny warily eyed several types of ectoguns lying on a steel cart at the side of the room. He knew they had almost perfected the models. Agent K lazily strode over to the chart and picked one of the guns up, turning it over and over in his hands.

"So, this is potentially the final version of our handheld ecto-gun. Lets have some fun, shall we?" He turned around to look at Danny again, who glared at Agent K. Quickly, the agent raised the gun and pointed it at Danny, pulling the trigger. The blast grazed Danny's arm and he barely flinched. When Agent K fired the weapon, Danny felt a slight pull at his core. He was accustomed to this feeling now, as the security systems in his chambers were powered through his signature. Those gave him a constant buzzing, pulling feeling in his chest at all times. He couldn't remember what it felt like to not be connected to the system. It was never extreme, the GIW needed him ready for battle, but it was enough to lower his performance ever so slightly. Despite his hatred for the GIW, Danny had to admit that their ability to tap into his energy without completely draining him was nice.

Agent K looked over the now smoking weapon and set it back on the cart. He picked up the next one, a slightly larger model with farther range and repeated the same action. This continued down the line of guns on the cart. After he set the last one back down, Agent K nodded and smiled, eyeing the selection of now completed weaponry. Danny was tired, since the weapons pulled a little from him each time, but he was still standing.

The GIW had made leaps and bounds with their technologies in the past decade. It was how they discovered Danny in the first place. Their tracking devices to hone in on Phantom's ectosignature were improved when Danny went to college, resulting in some close calls when he came home for the first time. Danny was used to finishing a fight and then having time to spare before the GIW tracked him down, but this time they arrived just after Danny had sucked the ghost into the thermos.

After Danny graduated college, the tracker became even sharper. It was now able to pick up traces of Phantom's ectosignature even when Danny was in human form. Eventually, the GIW tracked the signature down to Danny's home, realized that it was coming from him. They were confused and slow to respond at first, blaming this on faulty technology. But when every tracker began to do the same, their suspicion grew.

Team Phantom became aware of the GIW creeping closer and closer each day. Danny tried to find ways to suppress his signature even more, even trying out some of his parents' tech to suppress his ghost half. It was all to no avail as, one fateful night, the GIW came bursting into his home, taking him quietly off into the night.

They had their bases covered too. A fake story was released the following day about Danny going missing, a story that the GIW paid a large sum of money to the local papers to run. Unfortunately, it worked flawlessly. Sam and Tucker tried to protest; however they couldn't fully support their story of Danny being kidnapped by the GIW without revealing his secret. Sadly, with the public support of Phantom's disappearance (the GIW claimed Phantom was preparing to launch a ghost war, using the public's trust against them), Sam and Tucker knew revealing his secret would do more harm than good.

They had tried everything and exhausted all resources. The security was unbeatable; even Tucker couldn't crack it after years of trying. Valerie had inside knowledge but the information about Danny was only accessible by a select few employees. The GIW continued to manipulate the public with false reports and fake documents. It was beginning to seem hopeless.

Danny was led back into his sleeping quarters and was given a tray of food. The only bright side Danny found to his situation was that, for the most part, he remained unharmed (save for the slight drain from the weapons). At first, the weapons took so much energy from him that even an ectogun would leave him panting. How, the GIW learned how to maximize power with only a small amount of help from Danny's energy. With all of the weapons almost complete, Danny knew he was running out time before the GIW launched their war into the Ghost Zone, hoping to destroy ghosts once and for all. Despite Danny's pleas to stop and his explanation about how it would ultimately destroy both worlds, the GIW held fast to their convictions. And with their looming threats of eliminating every one Danny loved, he was left to cooperate and wait, hoping that maybe he could find a way to save everyone once the war started and he was outside of the GIW headquarters. For now, though, all Danny could do was wait.

* * *

Bethany breathed in deeply, standing in the middle of the training room. Clockwork watched from the side of the room, knowing what was to come. She pulled at the cold inside her, surprising herself when she actually felt it, and tried to view the world as nothing more than a blur. Suddenly, her body felt frozen and her eyes snapped open. She gazed around the room, finding it to waver slightly. It was as if she needed glasses but forgot to put them on; the room appeared fuzzy. Slowly, concentrating on not breaking her focus, she reached down and stuck her arm _through_ the floor. Gasping, she abruptly stood up and everything snapped back into focus. With wide eyes and a slight smile, Bethany turned to face Clockwork.

"I…I did it. You were right!" Clockwork smiled at her enthusiasm.

"Invisibility works in a similar way. You need to pull the cold out but instead focus on letting the energy surround only yourself, almost as if it were another layer of skin." Bethany concentrated again on the cold feeling, letting it surround her. She was surprised by how easily it came to her this time. She let herself be covered with her cold energy and watched with amazement as her hand disappeared from plain sight. Slowly, the rest of her body followed suit. When she came back into visibility, Bethany was beaming.

"Overshadowing someone works the same way. Once intangible, you can step inside someone else's body and allow your energy to flow. The person is an extension of yourself." Bethany listened intently, captivated with her newly discovered abilities. Clockwork had explained all she should be able to do in human form, making sure to mention that she may not have a full ghost form. After all, she was the first child born from a half-ghost, so no one really knew how it would work.

"Unfortunately, there is no one to practice with here, since it only works on humans. However I am confident that if you master all other abilities, then overshadowing will come naturally."

"And I need to be able to overshadow so I can get into the facility?" Clockwork nodded, recognizing her parents' intelligence from her quick understanding.

"The GIW want to wage a war on the Ghost Zone, using your father as the front lines. You can free him and eliminate this threat."

Clockwork patiently explained the plan for Bethany, waiting as she absorbed each step.

"Ghost families are very special. Like how humans share blood and genetics, ghosts share ectoplasm and ectosignatures. The frequency of Danny's ectosignature is in line with yours; it matches. Therefore, you can, let's say, borrow his energy. You just need to hone in on it."

Bethany mused over this information, staring intently into the wall behind Clockwork.

"This sounds extremely complicated. I just figured out how to use basic powers. How do you expect me to master this?" Clockwork smiled a small smile.

"We will practice and start small." Bethany let out a sigh. He had the upmost of faith in her. It made her nervous that she would screw something up.

"So if I can use his energy, this means what exactly?"

"The biggest obstacle to freeing your father is that the security for his chamber is run on his own ecto-energy. The same is true for most of the weapons. It is incredibly strong and can only be shut down once inside his chamber or by ending their use of Danny's energy. Since you can tap into his signature, you can effectively shut down the generators and weapons."

"How do they get his energy from him?" She asked worriedly. Clockwork only shook his head.

"They have discovered how to tap into a ghost's energy through its ectosignature. Their technology is modified to work through this, similar to a radio. It aligns with his ectosignature and the matched frequency allows the system to access the energy associated with that frequency. Thus, they can tap into your father's energy system through this signature, similar to how someone can tune into a station on the radio by switching to the right frequency."

"So since I can also tune into that frequency, then I can control the equipment. I can shut down the security. And I can also shut down the weaponry, stopping the war." The final pieces fell into place, as Bethany understood.

"So, how do I tap into his ectosignature?" She inquired. Clockwork guided her to the middle of the training room and turned to face her.

"This will require high focus and patience. I need you to trust what I instruct and to keep trying, no matter what. This step is the most important." Bethany nodded and he continued on.

"Close your eyes and focus on the Ghost Zone outside. Try and grasp a hold of its energy, feel its signature surrounding you." Bethany closed her eyes and reached out with her energy. She recognized her own energy and suddenly felt something else colliding with it. It felt like vibrations offset from her own, an energy on a different frequency than hers. She held onto it and memorized it.

"I want you to try and reach further into the Ghost Zone. Try and find other ghost's ectosignatures." Bethany did as he instructed, finding this step to be particularly difficult. She reached and concentrated, finding nothing but her own and the Ghost Zone's energies. After some time, she felt something off. It was distant and barely detectable, but she felt a third energy, different than both hers and the Zone's. She grabbed at it, bringing it forward. Bethany knew she had found another ghost. Clockwork smiled.

"When you are in the human realm, this will be easier, since the Ghost Zone energy will be less intense. All you need to do is bring forth your own energy and seek out your father's, letting it align with your own. Once you do this, it will be yours to control." Bethany opened her eyes and released the ectosignatures from her mind and body. She smiled and nodded to Clockwork, for the first time feeling confident that she might be able to pull this off.

* * *

Later that day, Bethany quickly walked into the viewing room. She made her way to Clockwork and stared at the floor as she conjured up the courage to ask him the question that had been on her mind all day. Finally, she spoke.

"Clockwork, what happens after this?" He knew exactly what she meant, of course, and turned to face her.

"Currently, I have your home town in a different timeline; one where you never arrived. Simply put, no one knows you or has any memory of you. You never existed in that world." Bethany's eyes widened and she snapped her head up at Clockwork. All this time, she simply figured her parents and Seth would assume she had gone missing. She had no idea that Clockwork had removed her from their lives altogether. He sensed her shock and continued explaining before she could respond.

"Should you choose to go back home after your father is freed, I can send you back to the same time as when I took you. No one will know the difference. Should you choose to stay in Amity Park, then your home town will remain in that timeline and no one will know you are even gone."

Bethany soon realized just how difficult this would be. Of course she wanted to go back to her home. That was where her life was. But was it fair to her real parents to re-enter their lives just to leave again? Especially when it was never their choice to have her taken away in the first place?

"Clockwork, do I….do I have to tell my real parents who I am?" He smiled a small, sad smile.

"That is a choice I will leave to you." She breathed a small sigh of relief. This way, she had more time to decide. Suddenly, Clockwork's words brought her back to her dream from the night before. _Choose._ She stiffened and decided to focus on freeing her dad first, letting the impending choice settle like led in her stomach to be dealt with later.


End file.
